Jerry from DIYAutoTune.com here-- the general consensus I'm seeing here is spot on I must say. You get out of a kit-built MegaSquirt system what you put into the build, installation, and tuning. The hardware will do just about anything you want it to. Once a system is properly installed and tuned, you'll see no weirdness out of the system, it just works. At the same time, and largely because of the low cost of entry, this opens the door for ANYONE to run a standalone EMS on their motor. Some of those people will do the homework, and take the time to do it right. When they find they did something that's less than optimal, they'll fix it and know it's not the ECU's problem but was a part of their learning curve. Dr. Hess's example of the IAT sensor he plans to move to get rid of the heat soak lean issue is a prime example, that's somewhat common for a user to put their IAT sensor where it was convenient, and not so much where it will be in the best environment to perform properly, and thankfully it's an easy fix. He'll relocate that, and his lean issue when the engine bay is super-hot will subside. I'm betting that's related to the other 'weirdness' issue he mentioned too, as properly sorted there just won't be any of that.
On the other hand, you'll always have some people that, smart or not, don't put the effort into it to properly install and tune the system. And again, you get out of it what you put into it.
As for cold start/warmup issues... you've got to tune your fuel/ignition tables, and then tune the cranking pulsewidth and warmup enrichments. You do this across all temp ranges you'll run into, and you won't have cold start problems, ever. If you expect the system to just fire the car up at 20 degrees when you tuned it in 95 degree weather and never tested/tuned at lower temps-- chances are you'll have a problem, because you didn't tune the car fully. You get out of it what you put into it.
We do of course have fully assembled and tested units if people want to cut out the assembly portion of the process. We also have plug-n-play models for Miatas, and more in the works. These units simply plug in where the factory computer used to, the come pre-mapped to fire up first turn of the key and even to drive away for a near-stock configuration (though we recommend fine tuning to verify it's ready to rock), and are as easy as any system out there to fine tune for your car, boost or no boost.
Bottom-line -- If the same user that ran into some of these types of learning curve issues, were to have started out by installing a big-name-high$ system, they would have run into the same exact learning curve. Difference is, it would have cost them 2x-10x the cost for the ECU, and they'd still have the learning curve to deal with. It's not rocket surgery, but it does require you, as someone put it above, to really think through how an engine works, how a fuel/air induction system works, how the parts in your forced induction system work, etc. You have to understand your powerplant well to properly engineer an EFI system for it. For most of our customers I'd imagine including most of you here, that's a bonus! You get pushed to understand how things work a bit more, and you'll be able to get more out of your combo because you do.
If you just want it to work and don't want to think about it, it still doesn't matter which EMS you use. MegaSquirt, Haltech, Fast, whatever. So long as you pay a shop to install it and tune it to perfection you shouldn't have to think about it too much. MegaSquirt will save you money on the hardware and do just as much as anything else out there, but the install/tuning can get expensive regardless of what system you use, and MS takes just as much time to install/tune as anything else. There's not a lot of margin in MS for shops currently, so they often push you towards a high-$ system that they'll make more money off of with a bigger margin on the hardware, and install/tune it for you. They are likely more familiar with these systems, as that's what they push so they can make the extra cash. Can't blame them really, they've got to keep their lights on and we sacrificed our margins to make the system affordable for YOU.
We're DIY AutoTune for a reason... heavy emphasis on the DIYer here. We'll provide you the tools to learn this stuff and have more in depth knowledge about how your engine works than any of your buddies/competitors do. You'll know your engine and your induction system well, why it works the way it does, how to make it better, and what benefits you can expect when you do so. And that knowledge really does equal power. Not to mention, it's a lot of fun!
If you want to learn more about tackling ANY EFI/EMS setup -- Matt Cramer and I wrote a book on EFI you can check out if you're interested, it's a practical hands-on approach at helping anyone understand how to choose, install, and tune an EMS, and it's had nothing but good reviews so far so I guess we did an ok job at it. You can check it out on our site, or on Amazon-- http://www.amazon.com/dp/1557885575?tag=httwwwdiycom-20&camp=14573&creative=327641&linkCode=as1&creativeASIN=1557885575&adid=1JNESZAXQT0DTJGRA5WA&